iFull wwPDB X-ray Structure Validation Report ○Oct 11, 2023 – 09:31 AM EDTPDB ID : 7N89Title : Room-temperature X-ray structure of SARS-CoV-2 main protease C145A mutant in complex with substrate Ac-SAVLQSGF-CONH2Authors : Kovalevsky, A.; Kneller, D.W.; Coates, L.
Deposited on : 2021-06-14
Resolution : 2.00 Å(reported)
This is a Full wwPDB X-ray Structure Validation Report for a publicly released PDB entry.
We welcome your comments at validation@mail.wwpdb.org
A user guide is available athttps://www.wwpdb.org/validation/2017/XrayValidationReportHelp
i symbol.
with specific help available everywhere you see the ○The types of validation reports are described at
http://www.wwpdb.org/validation/2017/FAQs#types.

i were used in the production of this report:
The following versions of software and data (see references ○)MolProbity
Mogul
Xtriage (Phenix)
EDS
Percentile statistics
Refmac
CCP4
Ideal geometry (proteins)
Ideal geometry (DNA, RNA)
Validation Pipeline (wwPDB-VP)

::
:
:
::
:
:
:
:

4.02b-467
1.8.5 (274361), CSD as541be (2020)1.13
2.35.1
20191225.v01 (using entries in the PDB archive December 25th 2019)
5.8.0158
7.0.044 (Gargrove)
Engh & Huber (2001)
Parkinson et al. (1996)
2.35.1

Page 2

1

Full wwPDB X-ray Structure Validation Report

7N89i
Overall quality at a glance ○The following experimental techniques were used to determine the structure:
X-RAY DIFFRACTION
The reported resolution of this entry is 2.00 Å.
Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.

MetricRf reeClashscore
Ramachandran outliers
Sidechain outliers
RSRZ outliers

Whole archive(#Entries)
130704141614138981138945127900Similar resolution(#Entries, resolution range(Å))
8085 (2.00-2.00)
9178 (2.00-2.00)
9054 (2.00-2.00)
9053 (2.00-2.00)
7900 (2.00-2.00)

The table below summarises the geometric issues observed across the polymeric chains and their
fit to the electron density. The red, orange, yellow and green segments of the lower bar indicate
the fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality
criteria respectively. A grey segment represents the fraction of residues that are not modelled.
The numeric value for each fraction is indicated below the corresponding segment, with a dot
representing fractions <=5% The upper red bar (where present) indicates the fraction of residues
that have poor fit to the electron density. The numeric value is given above the bar.
MolChain

Length1

A306

1

B306

2

C102

D10Quality of chain

Page 32

Full wwPDB X-ray Structure Validation Report

7N89i
Entry composition ○There are 3 unique types of molecules in this entry. The entry contains 5104 atoms, of which 0are hydrogens and 0 are deuteriums.
In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occupancy, the AltConf column contains the number of residues with at least one atom in alternate
conformation and the Trace column contains the number of residues modelled with at most 2atoms.
• Molecule 1 is a protein called 3C-like proteinase.
Mol

ChainResidues

1A306

1B306

Atoms
TotalCN
2369 1501 402
Total
CN2369 1501 402

O444
O444

S
22S22

ZeroOcc

AltConf

Trace

010010

There are 2 discrepancies between the modelled and reference sequences:Chain
A
B

Residue
145
145

Modelled
ALA
ALA

ActualCYS
CYSComment
engineered mutationengineered mutation

Reference
UNP P0DTD1
UNP P0DTD1• Molecule 2 is a protein called ACE-SER-ALA-VAL-LEU-GLN-SER-GLY-PHE-NH2.
Mol

Chain

Residues

2C

102D10Atoms
Total C N
6038 10Total C N
6038 10O
12O12ZeroOcc

AltConf

Trace001001• Molecule 3 is water.
MolChainResidues

3A125

3B120

3D1Atoms
Total O
125 125
Total O
120 120
Total O
11ZeroOcc

AltConf000000Page 4

3

Full wwPDB X-ray Structure Validation Report

7N89i
Residue-property plots ○These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. The
first graphic for a chain summarises the proportions of the various outlier classes displayed in thesecond graphic. The second graphic shows the sequence view annotated by issues in geometry andelectron density. Residues are color-coded according to the number of geometric quality criteria
for which they contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more.
A red dot above a residue indicates a poor fit to the electron density (RSRZ > 2). Stretches of 2or more consecutive residues without any outlier are shown as a green connector. Residues present
in the sample, but not in the model, are shown in grey.
• Molecule 1: 3C-like proteinase

•V303
T304
F305
Q306

R298

N277K269

N238

•
V233
A234
M235

I200

Q189

G179

•
Y154
D155

K137

R131

G109

K102

L89

•
V86

N72

R60

M49
L50

V36

S1

•

Chain A:• Molecule 1: 3C-like proteinase

•
•
V303
T304
F305
Q306

R298

I249

•
M235

L227

•
R222

D216

I200

•
Y154

K137

R131

P122

L115

G109

D92

R76

N72

I59
R60

D56

L27

S1

•
•

Chain B:

• Molecule 2: ACE-SER-ALA-VAL-LEU-GLN-SER-GLY-PHE-NH2

F9
NH210

ACE1

•

Chain C:• Molecule 2: ACE-SER-ALA-VAL-LEU-GLN-SER-GLY-PHE-NH2
Chain D:
There are no outlier residues recorded for this chain.

Page 54

Full wwPDB X-ray Structure Validation Report

7N89i
Data and refinement statistics ○Property
Space group
Cell constantsa, b, c, α, β, γResolution (Å)% Data completeness(in resolution range)
RmergeRsym< I/σ(I) > 1
Refinement program
R, Rf ree
Rf ree test set
Wilson B-factor (Å2 )Anisotropy
Bulk solvent ksol (e/Å3 ), Bsol (Å2 )L-test for twinning2
Estimated twinning fraction
Fo ,Fc correlation
Total number of atoms
Average B, all atoms (Å2 )ValueP147.65Å 54.10Å 60.50Å
66.88◦ 79.02◦ 88.52◦
22.13 – 2.00
29.29 – 2.00
93.6 (22.13-2.00)
93.7 (29.29-2.00)
0.10(Not available)
1.60 (at 2.00Å)PHENIX (1.17.1_3660: ???)
0.171 , 0.218
0.171 , 0.215
1744 reflections (5.06%)
25.5
0.089
0.34 , 44.1
< |L| > = 0.51, < L2 > = 0.35
No twinning to report.
0.96
5104
28.0

SourceDepositor
Depositor
Depositor
EDS
Depositor
EDS
Depositor
Depositor
Xtriage
Depositor
DepositorDCC
wwPDB-VP
Xtriage
Xtriage
EDS
Xtriage
XtriageEDS
wwPDB-VP
wwPDB-VP

Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Patterson
function is 8.37% of the height of the origin peak. No significant pseudotranslation is detected.

Intensities estimated from amplitudes.
Theoretical values of < |L| >, < L2 > for acentric reflections are 0.5, 0.333 respectively for untwinned datasets,
and 0.375, 0.2 for perfectly twinned datasets.
12Page 65

Full wwPDB X-ray Structure Validation Report

7N89i
Model quality ○5.1iStandard geometry ○Bond lengths and bond angles in the following residue types are not validated in this section: NH2,ACE
The Z score for a bond length (or angle) is the number of standard deviations the observed value
is removed from the expected value. A bond length (or angle) with |Z| > 5 is considered anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).
MolChain

1
1
2
2
All

A
BCDAllBond lengths
RMSZ #|Z| >50.29
0/24250.29
0/2425
0.31
0/57
0.33
0/57
0.290/4964

Bond angles
RMSZ #|Z| >50.48
0/32960.48
0/3296
0.44
0/76
0.49
0/76
0.48
0/6744

There are no bond length outliers.
There are no bond angle outliers.
There are no chirality outliers.
There are no planarity outliers.

5.2

iToo-close contacts ○In the following table, the Non-H and H(model) columns list the number of non-hydrogen atoms
and hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashes within
the asymmetric unit, whereas Symm-Clashes lists symmetry-related clashes.
Mol1122333AllChainABCDABDAll

Non-H
2369
2369
6060
12512015104

H(model)
00000000H(added)2319
2319
58580004754

Clashes
1070000017

Symm-Clashes
00000000

The all-atom clashscore is defined as the number of clashes found per 1000 atoms (includingPage 7

Full wwPDB X-ray Structure Validation Report

7N89

hydrogen atoms). The all-atom clashscore for this structure is 2.
All (17) close contacts within the same asymmetric unit are listed below, sorted by their clash
magnitude.
Atom-1Atom-2

1:A:298:ARG:HG3
1:B:298:ARG:HG3
1:A:155:ASP:HB3
1:B:115:LEU:HD11
1:B:131:ARG:HD3
1:A:131:ARG:HD3
1:A:109:GLY:HA2
1:A:298:ARG:HD2
1:A:49:MET:HB3
1:A:86:VAL:HG13
1:B:76:ARG:HG2
1:B:109:GLY:HA2
1:A:36:VAL:HB
1:B:227:LEU:HD12
1:A:102:LYS:HB2
1:A:233:VAL:HG11
1:B:56:ASP:O

1:A:303:VAL:HB
1:B:303:VAL:HB
1:A:306:GLN:HG3
1:B:122:PRO:HB3
1:B:137:LYS:HE2
1:A:137:LYS:HE2
1:A:200:ILE:HD13
1:A:305:PHE:HZ
1:A:189:GLN:HG3
1:A:179:GLY:HA2
1:B:92:ASP:CG
1:B:200:ILE:HD13
1:A:89:LEU:HB2
1:B:227:LEU:HA
1:A:102:LYS:HE3
1:A:269:LYS:HG3
1:B:59:ILE:HG22

Interatomic
distance (Å)
1.77
1.80
1.85
1.84
1.90
1.96
1.96
1.79
1.97
1.99
2.38
1.99
2.02
1.91
1.84
2.03
2.21

Clashoverlap (Å)
0.66
0.63
0.59
0.58
0.53
0.47
0.47
0.47
0.47
0.44
0.430.43
0.42
0.41
0.41
0.41
0.41

There are no symmetry-related clashes.

5.3

i
Torsion angles ○

5.3.1

i
Protein backbone ○In the following table, the Percentiles column shows the percent Ramachandran outliers of thechain as a percentile score with respect to all X-ray entries followed by that with respect to entries
of similar resolution.
The Analysed column shows the number of residues for which the backbone conformation wasanalysed, and the total number of residues.
MolChainAnalysed

Favoured

AllowedOutliers

Percentiles

1A

305/306 (100%)

298 (98%)

7 (2%)

0100100

1B

305/306 (100%)300 (98%)

5 (2%)

01001002C

8/10 (80%)

7 (88%)

1 (12%)

0100

100

2D

8/10 (80%)

6 (75%)

2 (25%)

0100 100
Continued on next page...

Page 8Full wwPDB X-ray Structure Validation Report

Continued from previous page...
Mol Chain
Analysed

Favoured

AllowedOutliers

All611 (98%)

15 (2%)

0All

626/632 (99%)

7N89

Percentiles
100

100

There are no Ramachandran outliers to report.
5.3.2

iProtein sidechains ○In the following table, the Percentiles column shows the percent sidechain outliers of the chain as apercentile score with respect to all X-ray entries followed by that with respect to entries of similar
resolution.
The Analysed column shows the number of residues for which the sidechain conformation was
analysed, and the total number of residues.
MolChainAnalysed

RotamericOutliers

Percentiles

1

A

263/262 (100%)

259 (98%)

4 (2%)

65

69

1

B

263/262 (100%)

259 (98%)

4 (2%)

65

69

2

C

6/6 (100%)

6 (100%)

0100

1002

D

6/6 (100%)

6 (100%)0100

100AllAll

538/536 (100%)530 (98%)

8 (2%)6569

All (8) residues with a non-rotameric sidechain are listed below:
Mol1111111
1Chain
AAAA
B
B
B
B

Res
60
154
23827727216
235249TypeARG
TYRASN
ASN
LEU
ASP
MET
ILE

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (1) suchsidechains are listed below:
Mol
1Chain
B

Res
119

TypeASNPage 95.3.3

Full wwPDB X-ray Structure Validation Reporti
RNA ○There are no RNA molecules in this entry.

5.4i
Non-standard residues in protein, DNA, RNA chains ○There are no non-standard protein/DNA/RNA residues in this entry.

5.5iCarbohydrates ○There are no monosaccharides in this entry.

5.6

i
Ligand geometry ○There are no ligands in this entry.

5.7

iOther polymers ○There are no such residues in this entry.

5.8i
Polymer linkage issues ○There are no chain breaks in this entry.

7N89

Page 10

6Full wwPDB X-ray Structure Validation Report

7N89

i
Fit of model and data ○6.1

iProtein, DNA and RNA chains ○In the following table, the column labelled ‘#RSRZ> 2’ contains the number (and percentage)of RSRZ outliers, followed by percent RSRZ outliers for the chain as percentile scores relative toall X-ray entries and entries of similar resolution. The OWAB column contains the minimum,median, 95th percentile and maximum values of the occupancy-weighted average B-factor perresidue. The column labelled ‘Q< 0.9’ lists the number of (and percentage) of residues with anaverage occupancy less than 0.9.
MolChainAnalysed<RSRZ>OWAB(Å2 )Q<0.91A

306/306 (100%)-0.28

5 (1%) 72

7016, 26, 43, 71

01

B306/306 (100%)-0.36

7 (2%) 60

59

16, 26, 45, 78

02

C

8/10 (80%)-0.24

1 (12%) 3

319, 24, 33, 56

02

D

8/10 (80%)

-0.35

0 100

10021, 24, 32, 56

0All

All

628/632 (99%)-0.32

13 (2%) 63

16, 26, 46, 78

0#RSRZ>262

All (13) RSRZ outliers are listed below:
Mol1211111111111

Chain
B
C
A
B
A
B
B
A
B
A
B
A
B

Res
154
9306306
154
305
222
235
235
72
605072

Type
TYR
PHE
GLN
GLN
TYR
PHE
ARG
METMETASN
ARG
LEU
ASN

RSRZ
4.2
4.0
3.9
3.8
3.7
2.9
2.8
2.5
2.5
2.5
2.2
2.1
2.0

6.2

i
Non-standard residues in protein, DNA, RNA chains ○There are no non-standard protein/DNA/RNA residues in this entry.

Page 11

6.3

Full wwPDB X-ray Structure Validation Reporti
Carbohydrates ○There are no monosaccharides in this entry.

6.4

i
Ligands ○There are no ligands in this entry.

6.5iOther polymers ○There are no such residues in this entry.

7N89